Drop support for Python 3.8

Author: mr-c

.github/workflows/ci-tests.yml

@@ -15,12 +15,12 @@ jobs:
   tox:
     name: CI tests via Tox
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13]
         step: [lint, unit, bandit, mypy]
 
     env:
@@ -35,8 +35,8 @@ jobs:
       - name: Set up Singularity
         if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce_3.11.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.11.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-noble_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-noble_amd64.deb
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -74,7 +74,7 @@ jobs:
   tox-style:
     name: CI linters via Tox
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -109,7 +109,7 @@ jobs:
 
   release_test:
     name: cwl-utils release test
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/tag_to_publish.yml

@@ -12,20 +12,20 @@ jobs:
   release_to_pypi:
     name: cwl-utils release test
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Singularity
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce_3.11.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.11.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-noble_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-noble_amd64.deb
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Cache for pip
         uses: actions/cache@v4

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 Style guide:
 - PEP-8 / format with ``black`` via ``make format``
-- Python 3.8+ compatible code
+- Python 3.9+ compatible code
 - PEP-484 type hints
 
 It is suggested that you run `git config blame.ignoreRevsFile .git-blame-ignore-revs`
@@ -17,7 +17,7 @@ Here's a rough guide (improvements are welcome!)
 - Install cwl-utils in the virtual environment: ``pip install -e .``
 - Check the version which might be different from the version installed in general on any system: ``pip show cwl-utils``
 - After you've made the changes, you can the complete test suite via tox: ``tox``
-	- If you want to run specific tests, say ``unit tests`` in Python 3.8, then: ``tox -e py38-unit``.
-	- Look at ``tox.ini`` for all available tests and runtimes
+	- If you want to run specific tests, say ``unit tests`` in Python 3.13, then: ``tox -e py313-unit``.
+	- Look at ``tox -l`` for all available tests and runtimes
 - If tests are passing, you can create a PR on ``cwl-utils`` GitHub repository.
 - After you're done working on the ``cwl-utils``, you can deactivate the virtual environment: ``deactivate``

Makefile

@@ -177,7 +177,7 @@ shellcheck: FORCE
 	shellcheck release-test.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py38-plus $^
+	pyupgrade --exit-zero-even-if-changed --py39-plus $^
 	auto-walrus $^
 
 release-test: FORCE

cwl_utils/__meta__.py

@@ -1,3 +1,3 @@
 # SPDX-License-Identifier: Apache-2.0
 """Global version number for the cwl_utils package."""
-__version__ = "0.34"
+__version__ = "0.35"

cwl_utils/cite_extract.py

@@ -2,7 +2,8 @@
 # SPDX-License-Identifier: Apache-2.0
 import argparse
 import sys
-from typing import Iterator, cast
+from collections.abc import Iterator
+from typing import cast
 
 import cwl_utils.parser as cwl
 

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -4,19 +4,8 @@
 """CWL Expression refactoring tool for CWL v1.0 ."""
 import copy
 import hashlib
-from collections.abc import Mapping
-from typing import (
-    Any,
-    Dict,
-    List,
-    MutableSequence,
-    Optional,
-    Sequence,
-    Tuple,
-    Type,
-    Union,
-    cast,
-)
+from collections.abc import Mapping, MutableSequence, Sequence
+from typing import Any, Optional, Union, cast
 
 from ruamel import yaml
 from schema_salad.sourceline import SourceLine
@@ -142,7 +131,7 @@ def get_expression(
 
 
 def etool_to_cltool(
-    etool: cwl.ExpressionTool, expressionLib: Optional[List[str]] = None
+    etool: cwl.ExpressionTool, expressionLib: Optional[list[str]] = None
 ) -> cwl.CommandLineTool:
     """Convert a ExpressionTool to a CommandLineTool."""
     inputs = yaml.comments.CommentedSeq()  # preserve the order
@@ -216,7 +205,7 @@ def traverse(
     inside: bool,
     skip_command_line1: bool,
     skip_command_line2: bool,
-) -> Tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
+) -> tuple[Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow], bool]:
     """Convert the given process and any subprocesses."""
     if not inside and isinstance(process, cwl.CommandLineTool):
         process = expand_stream_shortcuts(process)
@@ -330,7 +319,7 @@ def generate_etool_from_expr(
         Union[
             cwl.InputParameter,
             cwl.CommandInputParameter,
-            List[Union[cwl.InputParameter, cwl.CommandInputParameter]],
+            list[Union[cwl.InputParameter, cwl.CommandInputParameter]],
         ]
     ] = None,  # if the "self" input should be a different type than the "result" output
     extra_processes: Optional[
@@ -344,7 +333,7 @@ def generate_etool_from_expr(
             self_type = target
         if isinstance(self_type, list):
             new_type: Union[
-                List[Union[cwl.ArraySchema, cwl.InputRecordSchema]],
+                list[Union[cwl.ArraySchema, cwl.InputRecordSchema]],
                 Union[cwl.ArraySchema, cwl.InputRecordSchema],
             ] = [clean_type_ids(t.type_) for t in self_type if t.type_]
         elif self_type.type_:
@@ -420,7 +409,7 @@ def get_input_for_id(
     """Determine the CommandInputParameter for the given input name."""
     name = name.split("/")[-1]
 
-    for inp in cast(List[cwl.CommandInputParameter], tool.inputs):
+    for inp in cast(list[cwl.CommandInputParameter], tool.inputs):
         if inp.id and inp.id.split("#")[-1].split("/")[-1] == name:
             return inp
     if isinstance(tool, cwl.Workflow) and "/" in name:
@@ -437,7 +426,7 @@ def find_expressionLib(
     processes: Sequence[
         Union[cwl.CommandLineTool, cwl.Workflow, cwl.ExpressionTool, cwl.WorkflowStep]
     ]
-) -> Optional[List[str]]:
+) -> Optional[list[str]]:
     """
     Return the expressionLib from the highest priority InlineJavascriptRequirement.
 
@@ -448,7 +437,7 @@ def find_expressionLib(
         if process.requirements:
             for req in process.requirements:
                 if isinstance(req, cwl.InlineJavascriptRequirement):
-                    return cast(Optional[List[str]], copy.deepcopy(req.expressionLib))
+                    return cast(Optional[list[str]], copy.deepcopy(req.expressionLib))
     return None
 
 
@@ -457,15 +446,15 @@ def replace_expr_with_etool(
     name: str,
     workflow: cwl.Workflow,
     target: Union[cwl.CommandInputParameter, cwl.InputParameter],
-    source: Optional[Union[str, List[Any]]],
+    source: Optional[Union[str, list[Any]]],
     replace_etool: bool = False,
     extra_process: Optional[
         Union[cwl.Workflow, cwl.WorkflowStep, cwl.CommandLineTool]
     ] = None,
     source_type: Optional[cwl.CommandInputParameter] = None,
 ) -> None:
     """Modify the given workflow, replacing the expr with an standalone ExpressionTool."""
-    extra_processes: List[
+    extra_processes: list[
         Union[cwl.Workflow, cwl.WorkflowStep, cwl.CommandLineTool]
     ] = [workflow]
     if extra_process:
@@ -474,7 +463,7 @@ def replace_expr_with_etool(
         expr, target, source is None, source_type, extra_processes
     )
     if replace_etool:
-        processes: List[Union[cwl.WorkflowStep, cwl.Workflow, cwl.CommandLineTool]] = [
+        processes: list[Union[cwl.WorkflowStep, cwl.Workflow, cwl.CommandLineTool]] = [
             workflow
         ]
         if extra_process:
@@ -528,7 +517,7 @@ def empty_inputs(
         cwl.CommandLineTool, cwl.WorkflowStep, cwl.ExpressionTool, cwl.Workflow
     ],
     parent: Optional[cwl.Workflow] = None,
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Produce a mock input object for the given inputs."""
     result = {}
     if isinstance(process_or_step, cwl.Process):
@@ -662,22 +651,22 @@ def process_workflow_reqs_and_hints(
     #         and connecting all workflow inputs to the generated step
     modified = False
     inputs = empty_inputs(workflow)
-    generated_res_reqs: List[Tuple[str, Union[int, str]]] = []
-    generated_iwdr_reqs: List[Tuple[str, Union[int, str]]] = []
-    generated_envVar_reqs: List[Tuple[str, Union[int, str]]] = []
-    prop_reqs: Tuple[
+    generated_res_reqs: list[tuple[str, Union[int, str]]] = []
+    generated_iwdr_reqs: list[tuple[str, Union[int, str]]] = []
+    generated_envVar_reqs: list[tuple[str, Union[int, str]]] = []
+    prop_reqs: tuple[
         Union[
-            Type[cwl.EnvVarRequirement],
-            Type[cwl.ResourceRequirement],
-            Type[cwl.InitialWorkDirRequirement],
+            type[cwl.EnvVarRequirement],
+            type[cwl.ResourceRequirement],
+            type[cwl.InitialWorkDirRequirement],
         ],
         ...,
     ] = ()
     resourceReq: Optional[cwl.ResourceRequirement] = None
     envVarReq: Optional[cwl.EnvVarRequirement] = None
     iwdr: Optional[cwl.InitialWorkDirRequirement] = None
     if workflow.requirements is not None:
-        for req in cast(List[cwl.ProcessRequirement], workflow.requirements):
+        for req in cast(list[cwl.ProcessRequirement], workflow.requirements):
             if req and isinstance(req, cwl.EnvVarRequirement):
                 if req.envDef:
                     for index, envDef in enumerate(req.envDef):
@@ -994,9 +983,9 @@ def process_level_reqs(
     modified = False
     target_process = step.run
     inputs = empty_inputs(process)
-    generated_res_reqs: List[Tuple[str, str]] = []
-    generated_iwdr_reqs: List[Tuple[str, Union[int, str], Any]] = []
-    generated_envVar_reqs: List[Tuple[str, Union[int, str]]] = []
+    generated_res_reqs: list[tuple[str, str]] = []
+    generated_iwdr_reqs: list[tuple[str, Union[int, str], Any]] = []
+    generated_envVar_reqs: list[tuple[str, Union[int, str]]] = []
     if not step.id:
         return False
     step_name = step.id.split("#", 1)[-1]
@@ -1378,7 +1367,7 @@ def traverse_CommandLineTool(
                     }
                 ]
                 if outp.outputBinding.loadContents:
-                    cast(Dict[Any, Any], self)[0]["contents"] = "stuff"
+                    cast(dict[Any, Any], self)[0]["contents"] = "stuff"
                 expression = get_expression(outp.outputBinding.outputEval, inputs, self)
                 if expression:
                     modified = True
@@ -1635,7 +1624,7 @@ def replace_clt_hintreq_expr_with_etool(
 
 def cltool_inputs_to_etool_inputs(
     tool: cwl.CommandLineTool,
-) -> List[cwl.InputParameter]:
+) -> list[cwl.InputParameter]:
     """Copy CommandLineTool input objects into the equivalent ExpressionTool input objects."""
     inputs = yaml.comments.CommentedSeq()
     if tool.inputs:
@@ -1661,7 +1650,7 @@ def cltool_inputs_to_etool_inputs(
 
 def cltool_step_outputs_to_workflow_outputs(
     cltool_step: cwl.WorkflowStep, etool_step_id: str, etool_out_id: str
-) -> List[cwl.OutputParameter]:
+) -> list[cwl.OutputParameter]:
     """
     Copy CommandLineTool outputs into the equivalent Workflow output parameters.
 
@@ -1731,7 +1720,7 @@ def generate_etool_from_expr2(
  }"""
     )
     hints = None
-    procs: List[
+    procs: list[
         Union[cwl.CommandLineTool, cwl.ExpressionTool, cwl.Workflow, cwl.WorkflowStep]
     ] = []
     if process:
@@ -1820,12 +1809,12 @@ def traverse_step(
                     raise WorkflowException("target not found")
                 input_source_id = None
                 source_type: Optional[
-                    Union[List[cwl.InputParameter], cwl.InputParameter]
+                    Union[list[cwl.InputParameter], cwl.InputParameter]
                 ] = None
                 if inp.source:
                     if isinstance(inp.source, MutableSequence):
                         input_source_id = []
-                        source_types: List[cwl.InputParameter] = []
+                        source_types: list[cwl.InputParameter] = []
                         for source in inp.source:
                             source_id = source.split("#")[-1]
                             input_source_id.append(source_id)
@@ -1851,7 +1840,7 @@ def traverse_step(
                 # target.id = target.id.split('#')[-1]
                 if isinstance(original_process, cwl.ExpressionTool):
                     found_JSReq = False
-                    reqs: List[cwl.ProcessRequirement] = []
+                    reqs: list[cwl.ProcessRequirement] = []
                     if original_process.hints:
                         reqs.extend(original_process.hints)
                     if original_process.requirements:
@@ -1907,8 +1896,8 @@ def traverse_step(
 
 
 def workflow_step_to_InputParameters(
-    step_ins: List[cwl.WorkflowStepInput], parent: cwl.Workflow, except_in_id: str
-) -> List[cwl.InputParameter]:
+    step_ins: list[cwl.WorkflowStepInput], parent: cwl.Workflow, except_in_id: str
+) -> list[cwl.InputParameter]:
     """Create InputParameters to match the given WorkflowStep inputs."""
     params = []
     for inp in step_ins:
@@ -1947,10 +1936,10 @@ def replace_step_valueFrom_expr_with_etool(
     step: cwl.WorkflowStep,
     step_inp: cwl.WorkflowStepInput,
     original_process: Union[cwl.CommandLineTool, cwl.ExpressionTool],
-    original_step_ins: List[cwl.WorkflowStepInput],
-    source: Optional[Union[str, List[str]]],
+    original_step_ins: list[cwl.WorkflowStepInput],
+    source: Optional[Union[str, list[str]]],
     replace_etool: bool,
-    source_type: Optional[Union[cwl.InputParameter, List[cwl.InputParameter]]] = None,
+    source_type: Optional[Union[cwl.InputParameter, list[cwl.InputParameter]]] = None,
 ) -> None:
     """Replace a WorkflowStep level 'valueFrom' expression with a sibling ExpressionTool step."""
     if not step_inp.id:
@@ -1972,12 +1961,16 @@ def replace_step_valueFrom_expr_with_etool(
         [workflow, step],
     )
     if replace_etool:
-        processes = [
+        processes: list[
+            Union[
+                cwl.Workflow, cwl.CommandLineTool, cwl.ExpressionTool, cwl.WorkflowStep
+            ]
+        ] = [
             workflow,
             step,
-        ]  # type: List[Union[cwl.Workflow, cwl.CommandLineTool, cwl.ExpressionTool, cwl.WorkflowStep]]
+        ]
         cltool = etool_to_cltool(temp_etool, find_expressionLib(processes))
-        etool = cltool  # type: Union[cwl.ExpressionTool, cwl.CommandLineTool]
+        etool: Union[cwl.ExpressionTool, cwl.CommandLineTool] = cltool
     else:
         etool = temp_etool
     wf_step_inputs = copy.deepcopy(original_step_ins)
@@ -2026,7 +2019,7 @@ def traverse_workflow(
     replace_etool: bool,
     skip_command_line1: bool,
     skip_command_line2: bool,
-) -> Tuple[cwl.Workflow, bool]:
+) -> tuple[cwl.Workflow, bool]:
     """Traverse a workflow, processing each step."""
     modified = False
     for index, step in enumerate(workflow.steps):